sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2009-10-22
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1BR |
| AC: | P03367 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11686 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 51 % |
| B | 49 % |
| B-Factor: | 23.471 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.000 | 789.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.44 | 52.56 |
| According to VolSite | |
| HET Code: | JZQ |
|---|---|
| Formula: | C33H35F2N3O6S |
| Molecular weight: | 639.709 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.76 % |
| Polar Surface area: | 153.5 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 16.6993 | 22.8116 | 17.7092 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| O3 | OD2 | ASP- 25 | 2.78 | 151.31 | H-Bond (Protein Donor) |
| O5 | OD2 | ASP- 25 | 3.15 | 121.01 | H-Bond (Protein Donor) |
| O5 | OD2 | ASP- 25 | 2.89 | 126.72 | H-Bond (Ligand Donor) |
| N2 | O | GLY- 27 | 3.45 | 145.35 | H-Bond (Ligand Donor) |
| N4 | O | GLY- 27 | 3.2 | 153.01 | H-Bond (Ligand Donor) |
| C34 | CB | ALA- 28 | 3.51 | 0 | Hydrophobic |
| O7 | N | ASP- 29 | 3.11 | 171.58 | H-Bond (Protein Donor) |
| C39 | CB | ASP- 29 | 4.33 | 0 | Hydrophobic |
| C40 | CB | ASP- 29 | 3.68 | 0 | Hydrophobic |
| F1 | CB | ASP- 30 | 4.33 | 0 | Hydrophobic |
| C41 | CB | ASP- 30 | 4.48 | 0 | Hydrophobic |
| C37 | CB | ASP- 30 | 3.61 | 0 | Hydrophobic |
| C37 | CG2 | VAL- 32 | 3.89 | 0 | Hydrophobic |
| C38 | CG2 | VAL- 32 | 3.55 | 0 | Hydrophobic |
| F1 | CD1 | ILE- 47 | 3.83 | 0 | Hydrophobic |
| C42 | CB | ILE- 47 | 4.18 | 0 | Hydrophobic |
| C37 | CG2 | ILE- 47 | 3.81 | 0 | Hydrophobic |
| C41 | CG2 | ILE- 47 | 3.69 | 0 | Hydrophobic |
| C38 | CD1 | ILE- 47 | 3.87 | 0 | Hydrophobic |
| C36 | CB | ILE- 47 | 4.02 | 0 | Hydrophobic |
| S1 | CD1 | ILE- 50 | 3.51 | 0 | Hydrophobic |
| C33 | CG1 | ILE- 50 | 3.79 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 50 | 4.14 | 0 | Hydrophobic |
| C23 | CG1 | ILE- 50 | 3.86 | 0 | Hydrophobic |
| C25 | CB | PRO- 81 | 3.5 | 0 | Hydrophobic |
| C24 | CG | PRO- 81 | 3.78 | 0 | Hydrophobic |
| C29 | CB | VAL- 82 | 4.12 | 0 | Hydrophobic |
| C30 | CG2 | VAL- 82 | 4.28 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 82 | 4.09 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 82 | 3.78 | 0 | Hydrophobic |
| C29 | CG1 | ILE- 84 | 4.21 | 0 | Hydrophobic |
| C34 | CG2 | ILE- 84 | 4.26 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 4.1 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 84 | 3.72 | 0 | Hydrophobic |
| S1 | CD1 | ILE- 84 | 3.28 | 0 | Hydrophobic |
| O7 | O | HOH- 105 | 3.49 | 121.85 | H-Bond (Protein Donor) |
